Pathway Analysis for Cox regression Glmnet
John Zhuang
2024-06-17
library(multiMiR)## Welcome to multiMiR.
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## multiMiR database URL has been set to the
## default value: http://multimir.org/
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## Database Version: 2.3.0 Updated: 2020-04-15library(clusterProfiler)## ## clusterProfiler v4.12.2 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
##
## Please cite:
##
## T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan,
## X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal
## enrichment tool for interpreting omics data. The Innovation. 2021,
## 2(3):100141##
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## filterlibrary(org.Hs.eg.db)## Loading required package: AnnotationDbi## Loading required package: stats4## Loading required package: BiocGenerics##
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## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
## tapply, union, unique, unsplit, which.max, which.min## Loading required package: Biobase## Welcome to Bioconductor
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## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
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## select## library(stringr)
library(ggplot2)0. Loading of Results
A. List of all Gene names in the dataset
gene.names = readRDS("data/derived/unique_gene_names.rds")B. Selected Features
results.glmnet.cox = readRDS("data/sel_features/results_glmnet_cox_coef_1se.rds")
sel.features = results.glmnet.cox
sel.features## $fold3
## $fold3$elasticnet_0.5
## $fold3$elasticnet_0.5$dev
## hsa-mir-101-2 hsa-mir-125a hsa-mir-1277 hsa-mir-1307 hsa-mir-130b
## -0.143780726 -0.134165336 -0.448077046 0.373110532 0.106986296
## hsa-mir-199a-2 hsa-mir-199b hsa-mir-29c hsa-mir-3199-1 hsa-mir-320c-2
## 0.127672251 0.237477836 -0.051799128 -0.081638106 -0.267066343
## hsa-mir-3923 hsa-mir-513b hsa-mir-605 hsa-mir-664 hsa-mir-7-1
## 0.147642241 -0.053475381 -0.073428752 -0.940570385 0.539530827
## MRE11A.R2Gn AKT1.R2Gn RAD51.R2Gn MAPK9.R2Gn MAPK3.R2Gn
## 0.027384525 -0.015780032 0.479477264 -0.085717111 -0.634308840
## STMN1.R2Gn CHEK1.R2Gn CDK1.R2Gn EEF2K.R2Gn TYMS.R2Gn
## 0.006983371 0.622267874 0.185459762 -0.300795892 0.131317104
## FOXM1.R2Gn XIAP.R2Gn PREX1.R2Gn RET.R2Gn TFRC.RPPA
## 0.576229539 -1.263779736 -0.074469173 0.020331914 0.081977399
## CLDN7.g ANXA1.g
## -0.009327215 0.211844775
##
## $fold3$elasticnet_0.5$c
## hsa-mir-1307 hsa-mir-130b hsa-mir-199b hsa-mir-320c-2 hsa-mir-3923
## 0.032348699 0.168954949 0.120611119 -0.130133354 0.113022189
## hsa-mir-513b hsa-mir-605 hsa-mir-664 hsa-mir-7-1 RAD51.R2Gn
## -0.089747704 -0.021615310 -0.941792954 0.095432953 0.227265782
## MAPK9.R2Gn MAPK3.R2Gn CHEK1.R2Gn CDK1.R2Gn EEF2K.R2Gn
## -0.060114359 -0.450152165 0.146994963 0.218645287 -0.109938413
## TYMS.R2Gn FOXM1.R2Gn XIAP.R2Gn PREX1.R2Gn TFRC.RPPA
## 0.002027408 0.533289744 -0.865276041 -0.009236919 0.052186205
## ANXA1.g
## 0.067016750
##
##
## $fold3$lasso
## $fold3$lasso$dev
## hsa-mir-3923 hsa-mir-664 MAPK3.R2Gn FOXM1.R2Gn XIAP.R2Gn
## 0.0283139242 -1.7119840992 -0.0302255060 0.9724083977 -0.4313080991
## TFRC.RPPA
## 0.0006765457
##
## $fold3$lasso$c
## hsa-mir-320c-2 hsa-mir-3923 hsa-mir-664 MAPK3.R2Gn FOXM1.R2Gn
## -0.01983995 0.05010126 -1.68127653 -0.20066173 1.01943349
## XIAP.R2Gn TFRC.RPPA
## -0.68680559 0.01437263
##
##
##
## $fold5
## $fold5$elasticnet_0.5
## $fold5$elasticnet_0.5$dev
## numeric(0)
##
## $fold5$elasticnet_0.5$c
## hsa-mir-3923 hsa-mir-513b hsa-mir-664 CDK1.R2Gn FOXM1.R2Gn XIAP.R2Gn
## 0.04319868 -0.02301522 -0.69523526 0.08450855 0.31735481 -0.17014923
##
##
## $fold5$lasso
## $fold5$lasso$dev
## hsa-mir-3923 hsa-mir-664 MAPK3.R2Gn FOXM1.R2Gn XIAP.R2Gn
## 0.0283139242 -1.7119840992 -0.0302255060 0.9724083977 -0.4313080991
## TFRC.RPPA
## 0.0006765457
##
## $fold5$lasso$c
## hsa-mir-1277 hsa-mir-199b hsa-mir-3199-1 hsa-mir-320c-2 hsa-mir-330
## -2.88038031 0.92158572 -0.17472735 -1.85934550 0.18559755
## hsa-mir-3912 hsa-mir-3923 hsa-mir-605 hsa-mir-659 hsa-mir-7-1
## -1.17464142 0.74720999 -0.47819460 -0.43076862 5.75707121
## hsa-mir-873 PRKCD.R2Gn AKT1.R2Gn MAPK3.R2Gn WWTR1.R2Gn
## -0.16866896 -0.02331865 -0.03815669 -0.30593369 0.86778659
## TYMS.R2Gn FOXM1.R2Gn XIAP.R2Gn PREX1.R2Gn RET.R2Gn
## 1.00291281 1.19640658 -8.39856593 -0.44355829 2.35899817
## TFRC.RPPA CLDN7.g ANXA1.g
## 0.48479251 -0.10295925 1.02489560
##
##
##
## $fold10
## $fold10$elasticnet_0.5
## $fold10$elasticnet_0.5$dev
## hsa-mir-101-2 hsa-mir-125a hsa-mir-1277 hsa-mir-1307 hsa-mir-130b
## -0.005171816 -0.049259334 -0.147024699 0.204188473 0.151588631
## hsa-mir-199a-2 hsa-mir-199b hsa-mir-29c hsa-mir-3199-1 hsa-mir-320c-2
## 0.046253821 0.168289112 -0.006928248 -0.020207702 -0.192228371
## hsa-mir-3923 hsa-mir-513b hsa-mir-605 hsa-mir-664 hsa-mir-7-1
## 0.127817926 -0.078976945 -0.050266895 -0.948916208 0.286021290
## RAD51.R2Gn MAPK9.R2Gn MAPK3.R2Gn CHEK1.R2Gn CDK1.R2Gn
## 0.342007316 -0.076544205 -0.542538844 0.375489918 0.208250895
## EEF2K.R2Gn TYMS.R2Gn FOXM1.R2Gn XIAP.R2Gn PREX1.R2Gn
## -0.207113324 0.060684819 0.561982342 -1.056246305 -0.044114455
## TFRC.RPPA ANXA1.g
## 0.067949608 0.134325304
##
## $fold10$elasticnet_0.5$c
## hsa-mir-101-2 hsa-mir-125a hsa-mir-1277 hsa-mir-1307 hsa-mir-130b
## -0.077056038 -0.095520457 -0.304152528 0.296516093 0.130758687
## hsa-mir-199a-2 hsa-mir-199b hsa-mir-29c hsa-mir-3199-1 hsa-mir-320c-2
## 0.086497506 0.202242747 -0.025770943 -0.053535040 -0.229808987
## hsa-mir-3923 hsa-mir-513b hsa-mir-605 hsa-mir-664 hsa-mir-7-1
## 0.137474912 -0.065633768 -0.062185080 -0.949567413 0.412663607
## RAD51.R2Gn MAPK9.R2Gn MAPK3.R2Gn STMN1.R2Gn CHEK1.R2Gn
## 0.414282319 -0.078992679 -0.592334904 0.001022566 0.514261747
## CDK1.R2Gn EEF2K.R2Gn TYMS.R2Gn FOXM1.R2Gn XIAP.R2Gn
## 0.197959917 -0.255114112 0.096943992 0.571893341 -1.166807581
## PREX1.R2Gn TFRC.RPPA ANXA1.g
## -0.058933193 0.075364992 0.174931429
##
##
## $fold10$lasso
## $fold10$lasso$dev
## hsa-mir-320c-2 hsa-mir-3923 hsa-mir-664 MAPK3.R2Gn FOXM1.R2Gn
## -0.05949828 0.06474545 -1.65685970 -0.33221861 1.06976637
## XIAP.R2Gn TFRC.RPPA
## -0.91478154 0.02745507
##
## $fold10$lasso$c
## hsa-mir-664 FOXM1.R2Gn
## -0.415606866 0.0071356681. Convert microRNA to genes
Also remove the ending “.R2Gn” and “.RPPA” from gene names.
split.by.omic = function(variable.list) {
out.mRSG = variable.list[startsWith(variable.list, "hsa")]
out.R2Gn = variable.list[endsWith(variable.list, ".R2Gn")]
out.RPPA = variable.list[endsWith(variable.list, ".RPPA")]
#Mutations and gistict for glmnet only
out.M = variable.list[endsWith(variable.list, ".M")]
out.g = variable.list[endsWith(variable.list, ".g")]
out = list("miRNASeqGene" = out.mRSG,
"RNASeq2GeneNorm" = out.R2Gn,
"RPPAArray" = out.RPPA,
"Mutations" = out.M,
"gistict" = out.g)
out
}multiomics.to.GENES = function(sel.features, full.search = F, table = "validated", drop.miRNA = F) {
multiomics.list = split.by.omic(sel.features)
# Convert miRNASeqGene to target GENE names
# Skipped and returns an empty list instead of the list of select features,
# or if microRNA features are explicitly dropped (drop.miRNA = T).
# (Usually done when the features has only a few miRNA and unable to target any genes)
if (length(multiomics.list[[1]]) > 0 & !drop.miRNA) {
if (!full.search) { # Search only among the 198 genes in ACC, recommended
targets= get_multimir(mirna = multiomics.list[[1]],
target = gene.names,
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
} else { # Search the full dataset, not recommended.
# Use only if ACC gene search returns nothing or fails.
# Genes not in the ACC genes need to be manually removed.
targets= get_multimir(mirna = multiomics.list[[1]],
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
}
} else {
mRSG.target.genes = list()
}
#Remove suffix for Pathway Analysis Compatibility
R2Gn.genes = str_remove(multiomics.list[[2]], ".R2Gn")
RPPA.genes = str_remove(multiomics.list[[3]], ".RPPA")
M.genes = str_remove(multiomics.list[[4]], ".M")
g.genes = str_remove(multiomics.list[[5]], ".g")
#Join all cleaned-up genes are remove duplicates.
out1 = c(mRSG.target.genes, R2Gn.genes, RPPA.genes, M.genes, g.genes)
out = as.character(unique(out1))
out
}All microRNAs are dropped as they do not contribute enough to convert to genes.
geneNames <- list("3F_0.5_DEV"= multiomics.to.GENES(names(sel.features$fold3$elasticnet_0.5$dev), drop.miRNA = T),
"3F_0.5_C"= multiomics.to.GENES(names(sel.features$fold3$elasticnet_0.5$c), drop.miRNA = T),
"3F_1_DEV"= multiomics.to.GENES(names(sel.features$fold3$lasso$dev), drop.miRNA = T),
"3F_1_C"= multiomics.to.GENES(names(sel.features$fold3$lasso$c), drop.miRNA = T),
#"5F_0.5_DEV"= multiomics.to.GENES(names(sel.features$fold5$elasticnet_0.5$dev)), # 0 variables selected
"5F_0.5_C"= multiomics.to.GENES(names(sel.features$fold5$elasticnet_0.5$c), drop.miRNA = T),
"5F_1_DEV"=multiomics.to.GENES(names(sel.features$fold5$lasso$dev), drop.miRNA = T),
"5F_1_C"= multiomics.to.GENES(names(sel.features$fold5$lasso$c), drop.miRNA = T),
"10F_0.5_DEV"= multiomics.to.GENES(names(sel.features$fold10$elasticnet_0.5$dev), drop.miRNA = T),
"10F_0.5_C"= multiomics.to.GENES(names(sel.features$fold10$elasticnet_0.5$c), drop.miRNA = T),
"10F_1_DEV"= multiomics.to.GENES(names(sel.features$fold10$lasso$dev), drop.miRNA = T),
"10F_1_C"= multiomics.to.GENES(names(sel.features$fold10$lasso$c), drop.miRNA = T)
)geneNames## $`3F_0.5_DEV`
## [1] "MRE11A" "AKT1" "RAD51" "MAPK9" "MAPK3" "STMN1" "CHEK1" "CDK1"
## [9] "EEF2K" "TYMS" "FOXM1" "XIAP" "PREX1" "RET" "TFRC" "CLDN7"
## [17] "ANXA1"
##
## $`3F_0.5_C`
## [1] "RAD51" "MAPK9" "MAPK3" "CHEK1" "CDK1" "EEF2K" "TYMS" "FOXM1" "XIAP"
## [10] "PREX1" "TFRC" "ANXA1"
##
## $`3F_1_DEV`
## [1] "MAPK3" "FOXM1" "XIAP" "TFRC"
##
## $`3F_1_C`
## [1] "MAPK3" "FOXM1" "XIAP" "TFRC"
##
## $`5F_0.5_C`
## [1] "CDK1" "FOXM1" "XIAP"
##
## $`5F_1_DEV`
## [1] "MAPK3" "FOXM1" "XIAP" "TFRC"
##
## $`5F_1_C`
## [1] "PRKCD" "AKT1" "MAPK3" "WWTR1" "TYMS" "FOXM1" "XIAP" "PREX1" "RET"
## [10] "TFRC" "CLDN7" "ANXA1"
##
## $`10F_0.5_DEV`
## [1] "RAD51" "MAPK9" "MAPK3" "CHEK1" "CDK1" "EEF2K" "TYMS" "FOXM1" "XIAP"
## [10] "PREX1" "TFRC" "ANXA1"
##
## $`10F_0.5_C`
## [1] "RAD51" "MAPK9" "MAPK3" "STMN1" "CHEK1" "CDK1" "EEF2K" "TYMS" "FOXM1"
## [10] "XIAP" "PREX1" "TFRC" "ANXA1"
##
## $`10F_1_DEV`
## [1] "MAPK3" "FOXM1" "XIAP" "TFRC"
##
## $`10F_1_C`
## [1] "FOXM1"saveRDS(geneNames, file = "data/sel_features/gene_converted/genes_glmnet_cox_1se.rds")2. Pathway Analysis
A. GO Classification
ggo_MF <- list()#functional profile of a geneset for Molecular Function
ggo_BP <- list()#functional profile of a geneset for Biological Process
ggo_CC <- list()#functional profile of a geneset for Cellular Component
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ggo_MF[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="MF",
keyType="SYMBOL",
readable=TRUE)
ggo_BP[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="BP",
keyType="SYMBOL",
readable=TRUE)
ggo_CC[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="CC",
keyType="SYMBOL",
readable=TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11for(z in 1:length(geneNames)) {
print(head(ggo_MF[[z]]))
print(head(ggo_BP[[z]]))
print(head(ggo_CC[[z]]))
}## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/17
## GO:0003824 GO:0003824 catalytic activity 10 10/17
## GO:0005198 GO:0005198 structural molecule activity 1 1/17
## GO:0005215 GO:0005215 transporter activity 0 0/17
## GO:0005488 GO:0005488 binding 16 16/17
## GO:0009055 GO:0009055 electron transfer activity 0 0/17
## geneID
## GO:0003774
## GO:0003824 AKT1/RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/XIAP/RET
## GO:0005198 CLDN7
## GO:0005215
## GO:0005488 AKT1/RAD51/MAPK9/MAPK3/STMN1/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 3 3/17
## GO:0002376 GO:0002376 immune system process 8 8/17
## GO:0008152 GO:0008152 metabolic process 14 14/17
## GO:0009987 GO:0009987 cellular process 16 16/17
## GO:0016032 GO:0016032 viral process 3 3/17
## GO:0022414 GO:0022414 reproductive process 3 3/17
## geneID
## GO:0000003 AKT1/RAD51/CDK1
## GO:0002376 AKT1/MAPK9/MAPK3/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0008152 AKT1/RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0009987 AKT1/RAD51/MAPK9/MAPK3/STMN1/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0016032 AKT1/CDK1/TFRC
## GO:0022414 AKT1/RAD51/CDK1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 7 7/17
## GO:0044423 GO:0044423 virion component 0 0/17
## GO:0110165 GO:0110165 cellular anatomical entity 16 16/17
## geneID
## GO:0032991 AKT1/RAD51/CHEK1/CDK1/FOXM1/RET/TFRC
## GO:0044423
## GO:0110165 AKT1/RAD51/MAPK9/MAPK3/STMN1/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/12
## GO:0003824 GO:0003824 catalytic activity 8 8/12
## GO:0005198 GO:0005198 structural molecule activity 0 0/12
## GO:0005215 GO:0005215 transporter activity 0 0/12
## GO:0005488 GO:0005488 binding 12 12/12
## GO:0009055 GO:0009055 electron transfer activity 0 0/12
## geneID
## GO:0003774
## GO:0003824 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/XIAP
## GO:0005198
## GO:0005215
## GO:0005488 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 2 2/12
## GO:0002376 GO:0002376 immune system process 6 6/12
## GO:0008152 GO:0008152 metabolic process 12 12/12
## GO:0009987 GO:0009987 cellular process 12 12/12
## GO:0016032 GO:0016032 viral process 2 2/12
## GO:0022414 GO:0022414 reproductive process 2 2/12
## geneID
## GO:0000003 RAD51/CDK1
## GO:0002376 MAPK9/MAPK3/XIAP/PREX1/TFRC/ANXA1
## GO:0008152 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0009987 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0016032 CDK1/TFRC
## GO:0022414 RAD51/CDK1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 5 5/12
## GO:0044423 GO:0044423 virion component 0 0/12
## GO:0110165 GO:0110165 cellular anatomical entity 12 12/12
## geneID
## GO:0032991 RAD51/CHEK1/CDK1/FOXM1/TFRC
## GO:0044423
## GO:0110165 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/4
## GO:0003824 GO:0003824 catalytic activity 2 2/4
## GO:0005198 GO:0005198 structural molecule activity 0 0/4
## GO:0005215 GO:0005215 transporter activity 0 0/4
## GO:0005488 GO:0005488 binding 4 4/4
## GO:0009055 GO:0009055 electron transfer activity 0 0/4
## geneID
## GO:0003774
## GO:0003824 MAPK3/XIAP
## GO:0005198
## GO:0005215
## GO:0005488 MAPK3/FOXM1/XIAP/TFRC
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 0 0/4
## GO:0002376 GO:0002376 immune system process 3 3/4
## GO:0008152 GO:0008152 metabolic process 4 4/4
## GO:0009987 GO:0009987 cellular process 4 4/4
## GO:0016032 GO:0016032 viral process 1 1/4
## GO:0022414 GO:0022414 reproductive process 0 0/4
## geneID
## GO:0000003
## GO:0002376 MAPK3/XIAP/TFRC
## GO:0008152 MAPK3/FOXM1/XIAP/TFRC
## GO:0009987 MAPK3/FOXM1/XIAP/TFRC
## GO:0016032 TFRC
## GO:0022414
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 2 2/4
## GO:0044423 GO:0044423 virion component 0 0/4
## GO:0110165 GO:0110165 cellular anatomical entity 4 4/4
## geneID
## GO:0032991 FOXM1/TFRC
## GO:0044423
## GO:0110165 MAPK3/FOXM1/XIAP/TFRC
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/4
## GO:0003824 GO:0003824 catalytic activity 2 2/4
## GO:0005198 GO:0005198 structural molecule activity 0 0/4
## GO:0005215 GO:0005215 transporter activity 0 0/4
## GO:0005488 GO:0005488 binding 4 4/4
## GO:0009055 GO:0009055 electron transfer activity 0 0/4
## geneID
## GO:0003774
## GO:0003824 MAPK3/XIAP
## GO:0005198
## GO:0005215
## GO:0005488 MAPK3/FOXM1/XIAP/TFRC
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 0 0/4
## GO:0002376 GO:0002376 immune system process 3 3/4
## GO:0008152 GO:0008152 metabolic process 4 4/4
## GO:0009987 GO:0009987 cellular process 4 4/4
## GO:0016032 GO:0016032 viral process 1 1/4
## GO:0022414 GO:0022414 reproductive process 0 0/4
## geneID
## GO:0000003
## GO:0002376 MAPK3/XIAP/TFRC
## GO:0008152 MAPK3/FOXM1/XIAP/TFRC
## GO:0009987 MAPK3/FOXM1/XIAP/TFRC
## GO:0016032 TFRC
## GO:0022414
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 2 2/4
## GO:0044423 GO:0044423 virion component 0 0/4
## GO:0110165 GO:0110165 cellular anatomical entity 4 4/4
## geneID
## GO:0032991 FOXM1/TFRC
## GO:0044423
## GO:0110165 MAPK3/FOXM1/XIAP/TFRC
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/3
## GO:0003824 GO:0003824 catalytic activity 2 2/3
## GO:0005198 GO:0005198 structural molecule activity 0 0/3
## GO:0005215 GO:0005215 transporter activity 0 0/3
## GO:0005488 GO:0005488 binding 3 3/3
## GO:0009055 GO:0009055 electron transfer activity 0 0/3
## geneID
## GO:0003774
## GO:0003824 CDK1/XIAP
## GO:0005198
## GO:0005215
## GO:0005488 CDK1/FOXM1/XIAP
## GO:0009055
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 1 1/3 CDK1
## GO:0002376 GO:0002376 immune system process 1 1/3 XIAP
## GO:0008152 GO:0008152 metabolic process 3 3/3 CDK1/FOXM1/XIAP
## GO:0009987 GO:0009987 cellular process 3 3/3 CDK1/FOXM1/XIAP
## GO:0016032 GO:0016032 viral process 1 1/3 CDK1
## GO:0022414 GO:0022414 reproductive process 1 1/3 CDK1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 2 2/3
## GO:0044423 GO:0044423 virion component 0 0/3
## GO:0110165 GO:0110165 cellular anatomical entity 3 3/3
## geneID
## GO:0032991 CDK1/FOXM1
## GO:0044423
## GO:0110165 CDK1/FOXM1/XIAP
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/4
## GO:0003824 GO:0003824 catalytic activity 2 2/4
## GO:0005198 GO:0005198 structural molecule activity 0 0/4
## GO:0005215 GO:0005215 transporter activity 0 0/4
## GO:0005488 GO:0005488 binding 4 4/4
## GO:0009055 GO:0009055 electron transfer activity 0 0/4
## geneID
## GO:0003774
## GO:0003824 MAPK3/XIAP
## GO:0005198
## GO:0005215
## GO:0005488 MAPK3/FOXM1/XIAP/TFRC
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 0 0/4
## GO:0002376 GO:0002376 immune system process 3 3/4
## GO:0008152 GO:0008152 metabolic process 4 4/4
## GO:0009987 GO:0009987 cellular process 4 4/4
## GO:0016032 GO:0016032 viral process 1 1/4
## GO:0022414 GO:0022414 reproductive process 0 0/4
## geneID
## GO:0000003
## GO:0002376 MAPK3/XIAP/TFRC
## GO:0008152 MAPK3/FOXM1/XIAP/TFRC
## GO:0009987 MAPK3/FOXM1/XIAP/TFRC
## GO:0016032 TFRC
## GO:0022414
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 2 2/4
## GO:0044423 GO:0044423 virion component 0 0/4
## GO:0110165 GO:0110165 cellular anatomical entity 4 4/4
## geneID
## GO:0032991 FOXM1/TFRC
## GO:0044423
## GO:0110165 MAPK3/FOXM1/XIAP/TFRC
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/12
## GO:0003824 GO:0003824 catalytic activity 6 6/12
## GO:0005198 GO:0005198 structural molecule activity 1 1/12
## GO:0005215 GO:0005215 transporter activity 0 0/12
## GO:0005488 GO:0005488 binding 12 12/12
## GO:0009055 GO:0009055 electron transfer activity 0 0/12
## geneID
## GO:0003774
## GO:0003824 PRKCD/AKT1/MAPK3/TYMS/XIAP/RET
## GO:0005198 CLDN7
## GO:0005215
## GO:0005488 PRKCD/AKT1/MAPK3/WWTR1/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 1 1/12
## GO:0002376 GO:0002376 immune system process 8 8/12
## GO:0008152 GO:0008152 metabolic process 11 11/12
## GO:0009987 GO:0009987 cellular process 12 12/12
## GO:0016032 GO:0016032 viral process 2 2/12
## GO:0022414 GO:0022414 reproductive process 1 1/12
## geneID
## GO:0000003 AKT1
## GO:0002376 PRKCD/AKT1/MAPK3/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0008152 PRKCD/AKT1/MAPK3/WWTR1/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0009987 PRKCD/AKT1/MAPK3/WWTR1/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0016032 AKT1/TFRC
## GO:0022414 AKT1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 5 5/12
## GO:0044423 GO:0044423 virion component 0 0/12
## GO:0110165 GO:0110165 cellular anatomical entity 12 12/12
## geneID
## GO:0032991 AKT1/WWTR1/FOXM1/RET/TFRC
## GO:0044423
## GO:0110165 PRKCD/AKT1/MAPK3/WWTR1/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/12
## GO:0003824 GO:0003824 catalytic activity 8 8/12
## GO:0005198 GO:0005198 structural molecule activity 0 0/12
## GO:0005215 GO:0005215 transporter activity 0 0/12
## GO:0005488 GO:0005488 binding 12 12/12
## GO:0009055 GO:0009055 electron transfer activity 0 0/12
## geneID
## GO:0003774
## GO:0003824 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/XIAP
## GO:0005198
## GO:0005215
## GO:0005488 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 2 2/12
## GO:0002376 GO:0002376 immune system process 6 6/12
## GO:0008152 GO:0008152 metabolic process 12 12/12
## GO:0009987 GO:0009987 cellular process 12 12/12
## GO:0016032 GO:0016032 viral process 2 2/12
## GO:0022414 GO:0022414 reproductive process 2 2/12
## geneID
## GO:0000003 RAD51/CDK1
## GO:0002376 MAPK9/MAPK3/XIAP/PREX1/TFRC/ANXA1
## GO:0008152 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0009987 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0016032 CDK1/TFRC
## GO:0022414 RAD51/CDK1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 5 5/12
## GO:0044423 GO:0044423 virion component 0 0/12
## GO:0110165 GO:0110165 cellular anatomical entity 12 12/12
## geneID
## GO:0032991 RAD51/CHEK1/CDK1/FOXM1/TFRC
## GO:0044423
## GO:0110165 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/13
## GO:0003824 GO:0003824 catalytic activity 8 8/13
## GO:0005198 GO:0005198 structural molecule activity 0 0/13
## GO:0005215 GO:0005215 transporter activity 0 0/13
## GO:0005488 GO:0005488 binding 13 13/13
## GO:0009055 GO:0009055 electron transfer activity 0 0/13
## geneID
## GO:0003774
## GO:0003824 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/XIAP
## GO:0005198
## GO:0005215
## GO:0005488 RAD51/MAPK9/MAPK3/STMN1/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 2 2/13
## GO:0002376 GO:0002376 immune system process 6 6/13
## GO:0008152 GO:0008152 metabolic process 12 12/13
## GO:0009987 GO:0009987 cellular process 13 13/13
## GO:0016032 GO:0016032 viral process 2 2/13
## GO:0022414 GO:0022414 reproductive process 2 2/13
## geneID
## GO:0000003 RAD51/CDK1
## GO:0002376 MAPK9/MAPK3/XIAP/PREX1/TFRC/ANXA1
## GO:0008152 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0009987 RAD51/MAPK9/MAPK3/STMN1/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0016032 CDK1/TFRC
## GO:0022414 RAD51/CDK1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 5 5/13
## GO:0044423 GO:0044423 virion component 0 0/13
## GO:0110165 GO:0110165 cellular anatomical entity 13 13/13
## geneID
## GO:0032991 RAD51/CHEK1/CDK1/FOXM1/TFRC
## GO:0044423
## GO:0110165 RAD51/MAPK9/MAPK3/STMN1/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/4
## GO:0003824 GO:0003824 catalytic activity 2 2/4
## GO:0005198 GO:0005198 structural molecule activity 0 0/4
## GO:0005215 GO:0005215 transporter activity 0 0/4
## GO:0005488 GO:0005488 binding 4 4/4
## GO:0009055 GO:0009055 electron transfer activity 0 0/4
## geneID
## GO:0003774
## GO:0003824 MAPK3/XIAP
## GO:0005198
## GO:0005215
## GO:0005488 MAPK3/FOXM1/XIAP/TFRC
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 0 0/4
## GO:0002376 GO:0002376 immune system process 3 3/4
## GO:0008152 GO:0008152 metabolic process 4 4/4
## GO:0009987 GO:0009987 cellular process 4 4/4
## GO:0016032 GO:0016032 viral process 1 1/4
## GO:0022414 GO:0022414 reproductive process 0 0/4
## geneID
## GO:0000003
## GO:0002376 MAPK3/XIAP/TFRC
## GO:0008152 MAPK3/FOXM1/XIAP/TFRC
## GO:0009987 MAPK3/FOXM1/XIAP/TFRC
## GO:0016032 TFRC
## GO:0022414
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 2 2/4
## GO:0044423 GO:0044423 virion component 0 0/4
## GO:0110165 GO:0110165 cellular anatomical entity 4 4/4
## geneID
## GO:0032991 FOXM1/TFRC
## GO:0044423
## GO:0110165 MAPK3/FOXM1/XIAP/TFRC
## ID Description Count GeneRatio geneID
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/1
## GO:0003824 GO:0003824 catalytic activity 0 0/1
## GO:0005198 GO:0005198 structural molecule activity 0 0/1
## GO:0005215 GO:0005215 transporter activity 0 0/1
## GO:0005488 GO:0005488 binding 1 1/1 FOXM1
## GO:0009055 GO:0009055 electron transfer activity 0 0/1
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/1
## GO:0002376 GO:0002376 immune system process 0 0/1
## GO:0008152 GO:0008152 metabolic process 1 1/1 FOXM1
## GO:0009987 GO:0009987 cellular process 1 1/1 FOXM1
## GO:0016032 GO:0016032 viral process 0 0/1
## GO:0022414 GO:0022414 reproductive process 0 0/1
## ID Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex 1 1/1 FOXM1
## GO:0044423 GO:0044423 virion component 0 0/1
## GO:0110165 GO:0110165 cellular anatomical entity 1 1/1 FOXM1barplot(ggo_MF[[1]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_MF[[2]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_MF[[3]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 1, Deviance")
barplot(ggo_MF[[4]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 1, C-Index")
#barplot(ggo_MF[[5]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_MF[[5]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_MF[[6]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 1, Deviance")
barplot(ggo_MF[[7]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 1, C-Index")
barplot(ggo_MF[[8]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_MF[[9]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_MF[[10]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 1, Deviance")
barplot(ggo_MF[[11]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 1, C-Index")
barplot(ggo_BP[[1]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_BP[[2]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_BP[[3]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 1, Deviance")
barplot(ggo_BP[[4]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 1, C-Index")
#barplot(ggo_BP[[5]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_BP[[5]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_BP[[6]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 1, Deviance")
barplot(ggo_BP[[7]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 1, C-Index")
barplot(ggo_BP[[8]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_BP[[9]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_BP[[10]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 1, Deviance")
barplot(ggo_BP[[11]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 1, C-Index")
barplot(ggo_CC[[1]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_CC[[2]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_CC[[3]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 1, Deviance")
barplot(ggo_CC[[4]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 1, C-Index")
#barplot(ggo_CC[[5]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_CC[[5]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_CC[[6]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 1, Deviance")
barplot(ggo_CC[[7]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 1, C-Index")
barplot(ggo_CC[[8]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_CC[[9]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_CC[[10]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 1, Deviance")
barplot(ggo_CC[[11]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 1, C-Index")
B. GO Over-Representation
ego_MF <- list()#GO enrichment of a geneset for Molecular Function
ego_BP <- list()#GO enrichment of a geneset for Biological Process
ego_CC <- list()#GO enrichment of a geneset for Cellular Component
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ego_MF[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "MF",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_BP[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "BP",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_CC[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "CC",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11## No gene sets have size between 2 and 500 ...## --> return NULL...## No gene sets have size between 2 and 500 ...## --> return NULL...for(z in 1:(length(geneNames)-1)){ #11th element is null
print(head(ego_MF[[z]]))
print(head(ego_BP[[z]]))
print(head(ego_CC[[z]]))
}## ID Description
## GO:0004674 GO:0004674 protein serine/threonine kinase activity
## GO:0106310 GO:0106310 protein serine kinase activity
## GO:0004707 GO:0004707 MAP kinase activity
## GO:0035173 GO:0035173 histone kinase activity
## GO:0004712 GO:0004712 protein serine/threonine/tyrosine kinase activity
## GO:0030544 GO:0030544 Hsp70 protein binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0004674 6/16 427/18522 9.542515e-07 0.0001011507 4.921929e-05
## GO:0106310 5/16 363/18522 1.028418e-05 0.0005450614 2.652235e-04
## GO:0004707 2/16 16/18522 8.336346e-05 0.0029455088 1.433266e-03
## GO:0035173 2/16 23/18522 1.751391e-04 0.0046411863 2.258373e-03
## GO:0004712 2/16 43/18522 6.188351e-04 0.0131193047 6.383773e-03
## GO:0030544 2/16 51/18522 8.702575e-04 0.0153745500 7.481161e-03
## geneID Count
## GO:0004674 AKT1/MAPK9/MAPK3/CHEK1/CDK1/EEF2K 6
## GO:0106310 AKT1/MAPK9/MAPK3/CHEK1/CDK1 5
## GO:0004707 MAPK9/MAPK3 2
## GO:0035173 CHEK1/CDK1 2
## GO:0004712 AKT1/MAPK9 2
## GO:0030544 CDK1/TFRC 2
## ID Description GeneRatio
## GO:0051054 GO:0051054 positive regulation of DNA metabolic process 6/16
## GO:0046686 GO:0046686 response to cadmium ion 4/16
## GO:0010038 GO:0010038 response to metal ion 6/16
## GO:0042770 GO:0042770 signal transduction in response to DNA damage 5/16
## GO:0071241 GO:0071241 cellular response to inorganic substance 5/16
## GO:0097305 GO:0097305 response to alcohol 5/16
## BgRatio pvalue p.adjust qvalue
## GO:0051054 301/18888 1.091160e-07 0.0001151941 5.086625e-05
## GO:0046686 60/18888 1.627035e-07 0.0001151941 5.086625e-05
## GO:0010038 360/18888 3.134135e-07 0.0001310348 5.786105e-05
## GO:0042770 188/18888 3.701549e-07 0.0001310348 5.786105e-05
## GO:0071241 229/18888 9.823528e-07 0.0002782023 1.228458e-04
## GO:0097305 259/18888 1.800691e-06 0.0004249632 1.876510e-04
## geneID Count
## GO:0051054 AKT1/RAD51/MAPK3/CDK1/FOXM1/TFRC 6
## GO:0046686 AKT1/MAPK9/MAPK3/CDK1 4
## GO:0010038 AKT1/MAPK9/MAPK3/CDK1/EEF2K/TFRC 6
## GO:0042770 RAD51/MAPK3/CHEK1/CDK1/FOXM1 5
## GO:0071241 AKT1/RAD51/MAPK9/MAPK3/EEF2K 5
## GO:0097305 AKT1/RAD51/CDK1/TYMS/CLDN7 5
## ID Description GeneRatio BgRatio
## GO:0005769 GO:0005769 early endosome 4/16 428/19894
## GO:0000781 GO:0000781 chromosome, telomeric region 3/16 173/19894
## GO:0016323 GO:0016323 basolateral plasma membrane 3/16 255/19894
## GO:0016328 GO:0016328 lateral plasma membrane 2/16 68/19894
## GO:0009925 GO:0009925 basal plasma membrane 3/16 286/19894
## GO:0097122 GO:0097122 cyclin A2-CDK1 complex 1/16 2/19894
## pvalue p.adjust qvalue geneID Count
## GO:0005769 0.0003131011 0.01598376 0.01139194 MAPK3/RET/TFRC/ANXA1 4
## GO:0000781 0.0003329950 0.01598376 0.01139194 RAD51/CHEK1/CDK1 3
## GO:0016323 0.0010300925 0.01817677 0.01295494 TFRC/CLDN7/ANXA1 3
## GO:0016328 0.0013393677 0.01817677 0.01295494 CLDN7/ANXA1 2
## GO:0009925 0.0014331728 0.01817677 0.01295494 TFRC/CLDN7/ANXA1 3
## GO:0097122 0.0016079187 0.01817677 0.01295494 CDK1 1
## ID Description GeneRatio
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 5/12
## GO:0004707 GO:0004707 MAP kinase activity 2/12
## GO:0106310 GO:0106310 protein serine kinase activity 4/12
## GO:0035173 GO:0035173 histone kinase activity 2/12
## GO:0030544 GO:0030544 Hsp70 protein binding 2/12
## GO:0001618 GO:0001618 virus receptor activity 2/12
## BgRatio pvalue p.adjust qvalue
## GO:0004674 427/18522 4.408109e-06 0.0003702811 0.0001484837
## GO:0004707 16/18522 4.594242e-05 0.0017757774 0.0007120912
## GO:0106310 363/18522 6.342062e-05 0.0017757774 0.0007120912
## GO:0035173 23/18522 9.661815e-05 0.0020289811 0.0008136265
## GO:0030544 51/18522 4.820265e-04 0.0080980457 0.0032473366
## GO:0001618 79/18522 1.153123e-03 0.0108811215 0.0043633570
## geneID Count
## GO:0004674 MAPK9/MAPK3/CHEK1/CDK1/EEF2K 5
## GO:0004707 MAPK9/MAPK3 2
## GO:0106310 MAPK9/MAPK3/CHEK1/CDK1 4
## GO:0035173 CHEK1/CDK1 2
## GO:0030544 CDK1/TFRC 2
## GO:0001618 CDK1/TFRC 2
## ID Description GeneRatio
## GO:0042770 GO:0042770 signal transduction in response to DNA damage 5/12
## GO:0051054 GO:0051054 positive regulation of DNA metabolic process 5/12
## GO:0010038 GO:0010038 response to metal ion 5/12
## GO:0046686 GO:0046686 response to cadmium ion 3/12
## GO:0071241 GO:0071241 cellular response to inorganic substance 4/12
## GO:0048308 GO:0048308 organelle inheritance 2/12
## BgRatio pvalue p.adjust qvalue
## GO:0042770 188/18888 6.932499e-08 6.544279e-05 2.875163e-05
## GO:0051054 301/18888 7.184948e-07 3.391296e-04 1.489931e-04
## GO:0010038 360/18888 1.735716e-06 5.461720e-04 2.399551e-04
## GO:0046686 60/18888 6.569175e-06 1.550325e-03 6.811197e-04
## GO:0071241 229/18888 9.653169e-06 1.822518e-03 8.007049e-04
## GO:0048308 15/18888 3.867417e-05 5.215488e-03 2.291372e-03
## geneID Count
## GO:0042770 RAD51/MAPK3/CHEK1/CDK1/FOXM1 5
## GO:0051054 RAD51/MAPK3/CDK1/FOXM1/TFRC 5
## GO:0010038 MAPK9/MAPK3/CDK1/EEF2K/TFRC 5
## GO:0046686 MAPK9/MAPK3/CDK1 3
## GO:0071241 RAD51/MAPK9/MAPK3/EEF2K 4
## GO:0048308 MAPK3/CDK1 2
## ID Description GeneRatio
## GO:0000781 GO:0000781 chromosome, telomeric region 3/12
## GO:0000794 GO:0000794 condensed nuclear chromosome 2/12
## GO:0097122 GO:0097122 cyclin A2-CDK1 complex 1/12
## GO:0097125 GO:0097125 cyclin B1-CDK1 complex 1/12
## GO:0099182 GO:0099182 presynaptic intermediate filament cytoskeleton 1/12
## GO:0098687 GO:0098687 chromosomal region 3/12
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0000781 173/19894 0.0001342138 0.01167660 0.007346439 RAD51/CHEK1/CDK1 3
## GO:0000794 81/19894 0.0010524418 0.02098545 0.013203187 RAD51/CHEK1 2
## GO:0097122 2/19894 0.0012060603 0.02098545 0.013203187 CDK1 1
## GO:0097125 2/19894 0.0012060603 0.02098545 0.013203187 CDK1 1
## GO:0099182 2/19894 0.0012060603 0.02098545 0.013203187 RAD51 1
## GO:0098687 402/19894 0.0015730314 0.02280896 0.014350462 RAD51/CHEK1/CDK1 3
## ID
## GO:0004998 GO:0004998
## GO:0120283 GO:0120283
## GO:0004707 GO:0004707
## GO:0043027 GO:0043027
## GO:0004869 GO:0004869
## GO:0043028 GO:0043028
## Description
## GO:0004998 transferrin receptor activity
## GO:0120283 protein serine/threonine kinase binding
## GO:0004707 MAP kinase activity
## GO:0043027 cysteine-type endopeptidase inhibitor activity involved in apoptotic process
## GO:0004869 cysteine-type endopeptidase inhibitor activity
## GO:0043028 cysteine-type endopeptidase regulator activity involved in apoptotic process
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0004998 1/4 2/18522 0.0004318838 0.01295651 0.004091531 TFRC 1
## GO:0120283 1/4 7/18522 0.0015109813 0.02266472 0.007157280 XIAP 1
## GO:0004707 1/4 16/18522 0.0034511548 0.03234409 0.010213925 MAPK3 1
## GO:0043027 1/4 20/18522 0.0043125460 0.03234409 0.010213925 XIAP 1
## GO:0004869 1/4 37/18522 0.0079672300 0.03961505 0.012510017 XIAP 1
## GO:0043028 1/4 42/18522 0.0090402197 0.03961505 0.012510017 XIAP 1
## ID
## GO:0051054 GO:0051054
## GO:0032872 GO:0032872
## GO:0070302 GO:0070302
## GO:0051403 GO:0051403
## GO:0031098 GO:0031098
## GO:1902528 GO:1902528
## Description
## GO:0051054 positive regulation of DNA metabolic process
## GO:0032872 regulation of stress-activated MAPK cascade
## GO:0070302 regulation of stress-activated protein kinase signaling cascade
## GO:0051403 stress-activated MAPK cascade
## GO:0031098 stress-activated protein kinase signaling cascade
## GO:1902528 regulation of protein linear polyubiquitination
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0051054 3/4 301/18888 1.584016e-05 0.003341572 0.0009517791
## GO:0032872 2/4 35/18888 1.996811e-05 0.003341572 0.0009517791
## GO:0070302 2/4 38/18888 2.358757e-05 0.003341572 0.0009517791
## GO:0051403 2/4 50/18888 4.106724e-05 0.004363395 0.0012428244
## GO:0031098 2/4 59/18888 5.732355e-05 0.004872502 0.0013878333
## GO:1902528 1/4 2/18888 4.235157e-04 0.020667597 0.0058867459
## geneID Count
## GO:0051054 MAPK3/FOXM1/TFRC 3
## GO:0032872 MAPK3/FOXM1 2
## GO:0070302 MAPK3/FOXM1 2
## GO:0051403 MAPK3/FOXM1 2
## GO:0031098 MAPK3/FOXM1 2
## GO:1902528 XIAP 1
## ID Description GeneRatio BgRatio
## GO:1990712 GO:1990712 HFE-transferrin receptor complex 1/4 8/19894
## GO:0005769 GO:0005769 early endosome 2/4 428/19894
## GO:0031143 GO:0031143 pseudopodium 1/4 18/19894
## pvalue p.adjust qvalue geneID Count
## GO:1990712 0.001607676 0.03855515 0.01902392 TFRC 1
## GO:0005769 0.002692287 0.03855515 0.01902392 MAPK3/TFRC 2
## GO:0031143 0.003614545 0.03855515 0.01902392 MAPK3 1
## ID
## GO:0004998 GO:0004998
## GO:0120283 GO:0120283
## GO:0004707 GO:0004707
## GO:0043027 GO:0043027
## GO:0004869 GO:0004869
## GO:0043028 GO:0043028
## Description
## GO:0004998 transferrin receptor activity
## GO:0120283 protein serine/threonine kinase binding
## GO:0004707 MAP kinase activity
## GO:0043027 cysteine-type endopeptidase inhibitor activity involved in apoptotic process
## GO:0004869 cysteine-type endopeptidase inhibitor activity
## GO:0043028 cysteine-type endopeptidase regulator activity involved in apoptotic process
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0004998 1/4 2/18522 0.0004318838 0.01295651 0.004091531 TFRC 1
## GO:0120283 1/4 7/18522 0.0015109813 0.02266472 0.007157280 XIAP 1
## GO:0004707 1/4 16/18522 0.0034511548 0.03234409 0.010213925 MAPK3 1
## GO:0043027 1/4 20/18522 0.0043125460 0.03234409 0.010213925 XIAP 1
## GO:0004869 1/4 37/18522 0.0079672300 0.03961505 0.012510017 XIAP 1
## GO:0043028 1/4 42/18522 0.0090402197 0.03961505 0.012510017 XIAP 1
## ID
## GO:0051054 GO:0051054
## GO:0032872 GO:0032872
## GO:0070302 GO:0070302
## GO:0051403 GO:0051403
## GO:0031098 GO:0031098
## GO:1902528 GO:1902528
## Description
## GO:0051054 positive regulation of DNA metabolic process
## GO:0032872 regulation of stress-activated MAPK cascade
## GO:0070302 regulation of stress-activated protein kinase signaling cascade
## GO:0051403 stress-activated MAPK cascade
## GO:0031098 stress-activated protein kinase signaling cascade
## GO:1902528 regulation of protein linear polyubiquitination
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0051054 3/4 301/18888 1.584016e-05 0.003341572 0.0009517791
## GO:0032872 2/4 35/18888 1.996811e-05 0.003341572 0.0009517791
## GO:0070302 2/4 38/18888 2.358757e-05 0.003341572 0.0009517791
## GO:0051403 2/4 50/18888 4.106724e-05 0.004363395 0.0012428244
## GO:0031098 2/4 59/18888 5.732355e-05 0.004872502 0.0013878333
## GO:1902528 1/4 2/18888 4.235157e-04 0.020667597 0.0058867459
## geneID Count
## GO:0051054 MAPK3/FOXM1/TFRC 3
## GO:0032872 MAPK3/FOXM1 2
## GO:0070302 MAPK3/FOXM1 2
## GO:0051403 MAPK3/FOXM1 2
## GO:0031098 MAPK3/FOXM1 2
## GO:1902528 XIAP 1
## ID Description GeneRatio BgRatio
## GO:1990712 GO:1990712 HFE-transferrin receptor complex 1/4 8/19894
## GO:0005769 GO:0005769 early endosome 2/4 428/19894
## GO:0031143 GO:0031143 pseudopodium 1/4 18/19894
## pvalue p.adjust qvalue geneID Count
## GO:1990712 0.001607676 0.03855515 0.01902392 TFRC 1
## GO:0005769 0.002692287 0.03855515 0.01902392 MAPK3/TFRC 2
## GO:0031143 0.003614545 0.03855515 0.01902392 MAPK3 1
## ID
## GO:0120283 GO:0120283
## GO:0008353 GO:0008353
## GO:0043027 GO:0043027
## GO:0035173 GO:0035173
## GO:0140994 GO:0140994
## GO:0004693 GO:0004693
## Description
## GO:0120283 protein serine/threonine kinase binding
## GO:0008353 RNA polymerase II CTD heptapeptide repeat kinase activity
## GO:0043027 cysteine-type endopeptidase inhibitor activity involved in apoptotic process
## GO:0035173 histone kinase activity
## GO:0140994 RNA polymerase II CTD heptapeptide repeat modifying activity
## GO:0004693 cyclin-dependent protein serine/threonine kinase activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0120283 1/3 7/18522 0.001133420 0.01860828 0.005596474 XIAP 1
## GO:0008353 1/3 10/18522 0.001618909 0.01860828 0.005596474 CDK1 1
## GO:0043027 1/3 20/18522 0.003236069 0.01860828 0.005596474 XIAP 1
## GO:0035173 1/3 23/18522 0.003720876 0.01860828 0.005596474 CDK1 1
## GO:0140994 1/3 23/18522 0.003720876 0.01860828 0.005596474 CDK1 1
## GO:0004693 1/3 29/18522 0.004690019 0.01860828 0.005596474 CDK1 1
## ID Description
## GO:0000086 GO:0000086 G2/M transition of mitotic cell cycle
## GO:0044839 GO:0044839 cell cycle G2/M phase transition
## GO:0042770 GO:0042770 signal transduction in response to DNA damage
## GO:1902528 GO:1902528 regulation of protein linear polyubiquitination
## GO:1902530 GO:1902530 positive regulation of protein linear polyubiquitination
## GO:0014038 GO:0014038 regulation of Schwann cell differentiation
## GeneRatio BgRatio pvalue p.adjust qvalue geneID
## GO:0000086 2/3 136/18888 0.0001536688 0.01772460 0.002808652 CDK1/FOXM1
## GO:0044839 2/3 152/18888 0.0001919938 0.01772460 0.002808652 CDK1/FOXM1
## GO:0042770 2/3 188/18888 0.0002937047 0.01772460 0.002808652 CDK1/FOXM1
## GO:1902528 1/3 2/18888 0.0003176452 0.01772460 0.002808652 XIAP
## GO:1902530 1/3 2/18888 0.0003176452 0.01772460 0.002808652 XIAP
## GO:0014038 1/3 4/18888 0.0006352231 0.02084585 0.003303247 CDK1
## Count
## GO:0000086 2
## GO:0044839 2
## GO:0042770 2
## GO:1902528 1
## GO:1902530 1
## GO:0014038 1
## ID Description
## GO:0097122 GO:0097122 cyclin A2-CDK1 complex
## GO:0097125 GO:0097125 cyclin B1-CDK1 complex
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0005876 GO:0005876 spindle microtubule
## GO:1902554 GO:1902554 serine/threonine protein kinase complex
## GO:1902911 GO:1902911 protein kinase complex
## GeneRatio BgRatio pvalue p.adjust qvalue geneID
## GO:0097122 1/3 2/19894 0.0003015833 0.002111083 0.0006349122 CDK1
## GO:0097125 1/3 2/19894 0.0003015833 0.002111083 0.0006349122 CDK1
## GO:0000307 1/3 56/19894 0.0084214303 0.039300008 0.0118195514 CDK1
## GO:0005876 1/3 82/19894 0.0123152550 0.043103393 0.0129634264 CDK1
## GO:1902554 1/3 136/19894 0.0203698303 0.047596740 0.0143148091 CDK1
## GO:1902911 1/3 150/19894 0.0224508810 0.047596740 0.0143148091 CDK1
## Count
## GO:0097122 1
## GO:0097125 1
## GO:0000307 1
## GO:0005876 1
## GO:1902554 1
## GO:1902911 1
## ID
## GO:0004998 GO:0004998
## GO:0120283 GO:0120283
## GO:0004707 GO:0004707
## GO:0043027 GO:0043027
## GO:0004869 GO:0004869
## GO:0043028 GO:0043028
## Description
## GO:0004998 transferrin receptor activity
## GO:0120283 protein serine/threonine kinase binding
## GO:0004707 MAP kinase activity
## GO:0043027 cysteine-type endopeptidase inhibitor activity involved in apoptotic process
## GO:0004869 cysteine-type endopeptidase inhibitor activity
## GO:0043028 cysteine-type endopeptidase regulator activity involved in apoptotic process
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0004998 1/4 2/18522 0.0004318838 0.01295651 0.004091531 TFRC 1
## GO:0120283 1/4 7/18522 0.0015109813 0.02266472 0.007157280 XIAP 1
## GO:0004707 1/4 16/18522 0.0034511548 0.03234409 0.010213925 MAPK3 1
## GO:0043027 1/4 20/18522 0.0043125460 0.03234409 0.010213925 XIAP 1
## GO:0004869 1/4 37/18522 0.0079672300 0.03961505 0.012510017 XIAP 1
## GO:0043028 1/4 42/18522 0.0090402197 0.03961505 0.012510017 XIAP 1
## ID
## GO:0051054 GO:0051054
## GO:0032872 GO:0032872
## GO:0070302 GO:0070302
## GO:0051403 GO:0051403
## GO:0031098 GO:0031098
## GO:1902528 GO:1902528
## Description
## GO:0051054 positive regulation of DNA metabolic process
## GO:0032872 regulation of stress-activated MAPK cascade
## GO:0070302 regulation of stress-activated protein kinase signaling cascade
## GO:0051403 stress-activated MAPK cascade
## GO:0031098 stress-activated protein kinase signaling cascade
## GO:1902528 regulation of protein linear polyubiquitination
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0051054 3/4 301/18888 1.584016e-05 0.003341572 0.0009517791
## GO:0032872 2/4 35/18888 1.996811e-05 0.003341572 0.0009517791
## GO:0070302 2/4 38/18888 2.358757e-05 0.003341572 0.0009517791
## GO:0051403 2/4 50/18888 4.106724e-05 0.004363395 0.0012428244
## GO:0031098 2/4 59/18888 5.732355e-05 0.004872502 0.0013878333
## GO:1902528 1/4 2/18888 4.235157e-04 0.020667597 0.0058867459
## geneID Count
## GO:0051054 MAPK3/FOXM1/TFRC 3
## GO:0032872 MAPK3/FOXM1 2
## GO:0070302 MAPK3/FOXM1 2
## GO:0051403 MAPK3/FOXM1 2
## GO:0031098 MAPK3/FOXM1 2
## GO:1902528 XIAP 1
## ID Description GeneRatio BgRatio
## GO:1990712 GO:1990712 HFE-transferrin receptor complex 1/4 8/19894
## GO:0005769 GO:0005769 early endosome 2/4 428/19894
## GO:0031143 GO:0031143 pseudopodium 1/4 18/19894
## pvalue p.adjust qvalue geneID Count
## GO:1990712 0.001607676 0.03855515 0.01902392 TFRC 1
## GO:0005769 0.002692287 0.03855515 0.01902392 MAPK3/TFRC 2
## GO:0031143 0.003614545 0.03855515 0.01902392 MAPK3 1
## ID
## GO:0004998 GO:0004998
## GO:0106310 GO:0106310
## GO:0004857 GO:0004857
## GO:0072341 GO:0072341
## GO:0004699 GO:0004699
## GO:0004674 GO:0004674
## Description
## GO:0004998 transferrin receptor activity
## GO:0106310 protein serine kinase activity
## GO:0004857 enzyme inhibitor activity
## GO:0072341 modified amino acid binding
## GO:0004699 diacylglycerol-dependent, calcium-independent serine/threonine kinase activity
## GO:0004674 protein serine/threonine kinase activity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0004998 1/12 2/18522 0.001295372 0.02813253 0.01429602
## GO:0106310 3/12 363/18522 0.001440011 0.02813253 0.01429602
## GO:0004857 3/12 389/18522 0.001756270 0.02813253 0.01429602
## GO:0072341 2/12 101/18522 0.001875154 0.02813253 0.01429602
## GO:0004699 1/12 3/18522 0.001942480 0.02813253 0.01429602
## GO:0004674 3/12 427/18522 0.002292264 0.02813253 0.01429602
## geneID Count
## GO:0004998 TFRC 1
## GO:0106310 PRKCD/AKT1/MAPK3 3
## GO:0004857 AKT1/XIAP/ANXA1 3
## GO:0072341 TYMS/ANXA1 2
## GO:0004699 PRKCD 1
## GO:0004674 PRKCD/AKT1/MAPK3 3
## ID Description
## GO:1900182 GO:1900182 positive regulation of protein localization to nucleus
## GO:0051054 GO:0051054 positive regulation of DNA metabolic process
## GO:1900180 GO:1900180 regulation of protein localization to nucleus
## GO:0042119 GO:0042119 neutrophil activation
## GO:0032079 GO:0032079 positive regulation of endodeoxyribonuclease activity
## GO:0050900 GO:0050900 leukocyte migration
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:1900182 4/12 94/18888 2.761675e-07 0.0003628840 0.0001293627
## GO:0051054 5/12 301/18888 7.184948e-07 0.0004720511 0.0001682791
## GO:1900180 4/12 144/18888 1.529511e-06 0.0005830354 0.0002078433
## GO:0042119 3/12 42/18888 2.218042e-06 0.0005830354 0.0002078433
## GO:0032079 2/12 4/18888 2.218552e-06 0.0005830354 0.0002078433
## GO:0050900 5/12 396/18888 2.771090e-06 0.0006068688 0.0002163395
## geneID Count
## GO:1900182 PRKCD/AKT1/WWTR1/TFRC 4
## GO:0051054 PRKCD/AKT1/MAPK3/FOXM1/TFRC 5
## GO:1900180 PRKCD/AKT1/WWTR1/TFRC 4
## GO:0042119 PRKCD/PREX1/ANXA1 3
## GO:0032079 PRKCD/AKT1 2
## GO:0050900 AKT1/MAPK3/PREX1/RET/ANXA1 5
## ID Description GeneRatio BgRatio
## GO:0005769 GO:0005769 early endosome 4/12 428/19894
## GO:0016323 GO:0016323 basolateral plasma membrane 3/12 255/19894
## GO:0009925 GO:0009925 basal plasma membrane 3/12 286/19894
## GO:0045178 GO:0045178 basal part of cell 3/12 305/19894
## GO:0016328 GO:0016328 lateral plasma membrane 2/12 68/19894
## pvalue p.adjust qvalue geneID Count
## GO:0005769 9.118026e-05 0.006291438 0.004894940 MAPK3/RET/TFRC/ANXA1 4
## GO:0016323 4.203296e-04 0.010255994 0.007979492 TFRC/CLDN7/ANXA1 3
## GO:0009925 5.875358e-04 0.010255994 0.007979492 TFRC/CLDN7/ANXA1 3
## GO:0045178 7.084455e-04 0.010255994 0.007979492 TFRC/CLDN7/ANXA1 3
## GO:0016328 7.431879e-04 0.010255994 0.007979492 CLDN7/ANXA1 2
## ID Description GeneRatio
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 5/12
## GO:0004707 GO:0004707 MAP kinase activity 2/12
## GO:0106310 GO:0106310 protein serine kinase activity 4/12
## GO:0035173 GO:0035173 histone kinase activity 2/12
## GO:0030544 GO:0030544 Hsp70 protein binding 2/12
## GO:0001618 GO:0001618 virus receptor activity 2/12
## BgRatio pvalue p.adjust qvalue
## GO:0004674 427/18522 4.408109e-06 0.0003702811 0.0001484837
## GO:0004707 16/18522 4.594242e-05 0.0017757774 0.0007120912
## GO:0106310 363/18522 6.342062e-05 0.0017757774 0.0007120912
## GO:0035173 23/18522 9.661815e-05 0.0020289811 0.0008136265
## GO:0030544 51/18522 4.820265e-04 0.0080980457 0.0032473366
## GO:0001618 79/18522 1.153123e-03 0.0108811215 0.0043633570
## geneID Count
## GO:0004674 MAPK9/MAPK3/CHEK1/CDK1/EEF2K 5
## GO:0004707 MAPK9/MAPK3 2
## GO:0106310 MAPK9/MAPK3/CHEK1/CDK1 4
## GO:0035173 CHEK1/CDK1 2
## GO:0030544 CDK1/TFRC 2
## GO:0001618 CDK1/TFRC 2
## ID Description GeneRatio
## GO:0042770 GO:0042770 signal transduction in response to DNA damage 5/12
## GO:0051054 GO:0051054 positive regulation of DNA metabolic process 5/12
## GO:0010038 GO:0010038 response to metal ion 5/12
## GO:0046686 GO:0046686 response to cadmium ion 3/12
## GO:0071241 GO:0071241 cellular response to inorganic substance 4/12
## GO:0048308 GO:0048308 organelle inheritance 2/12
## BgRatio pvalue p.adjust qvalue
## GO:0042770 188/18888 6.932499e-08 6.544279e-05 2.875163e-05
## GO:0051054 301/18888 7.184948e-07 3.391296e-04 1.489931e-04
## GO:0010038 360/18888 1.735716e-06 5.461720e-04 2.399551e-04
## GO:0046686 60/18888 6.569175e-06 1.550325e-03 6.811197e-04
## GO:0071241 229/18888 9.653169e-06 1.822518e-03 8.007049e-04
## GO:0048308 15/18888 3.867417e-05 5.215488e-03 2.291372e-03
## geneID Count
## GO:0042770 RAD51/MAPK3/CHEK1/CDK1/FOXM1 5
## GO:0051054 RAD51/MAPK3/CDK1/FOXM1/TFRC 5
## GO:0010038 MAPK9/MAPK3/CDK1/EEF2K/TFRC 5
## GO:0046686 MAPK9/MAPK3/CDK1 3
## GO:0071241 RAD51/MAPK9/MAPK3/EEF2K 4
## GO:0048308 MAPK3/CDK1 2
## ID Description GeneRatio
## GO:0000781 GO:0000781 chromosome, telomeric region 3/12
## GO:0000794 GO:0000794 condensed nuclear chromosome 2/12
## GO:0097122 GO:0097122 cyclin A2-CDK1 complex 1/12
## GO:0097125 GO:0097125 cyclin B1-CDK1 complex 1/12
## GO:0099182 GO:0099182 presynaptic intermediate filament cytoskeleton 1/12
## GO:0098687 GO:0098687 chromosomal region 3/12
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0000781 173/19894 0.0001342138 0.01167660 0.007346439 RAD51/CHEK1/CDK1 3
## GO:0000794 81/19894 0.0010524418 0.02098545 0.013203187 RAD51/CHEK1 2
## GO:0097122 2/19894 0.0012060603 0.02098545 0.013203187 CDK1 1
## GO:0097125 2/19894 0.0012060603 0.02098545 0.013203187 CDK1 1
## GO:0099182 2/19894 0.0012060603 0.02098545 0.013203187 RAD51 1
## GO:0098687 402/19894 0.0015730314 0.02280896 0.014350462 RAD51/CHEK1/CDK1 3
## ID Description GeneRatio
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 5/13
## GO:0004707 GO:0004707 MAP kinase activity 2/13
## GO:0106310 GO:0106310 protein serine kinase activity 4/13
## GO:0035173 GO:0035173 histone kinase activity 2/13
## GO:0030544 GO:0030544 Hsp70 protein binding 2/13
## GO:0001618 GO:0001618 virus receptor activity 2/13
## BgRatio pvalue p.adjust qvalue
## GO:0004674 427/18522 7.027626e-06 0.0005973482 0.0002589125
## GO:0004707 16/18522 5.426823e-05 0.0023063998 0.0009996779
## GO:0106310 363/18522 9.019385e-05 0.0024245997 0.0010509101
## GO:0035173 23/18522 1.140988e-04 0.0024245997 0.0010509101
## GO:0030544 51/18522 5.686647e-04 0.0096673002 0.0041901611
## GO:0001618 79/18522 1.359016e-03 0.0119278915 0.0051699839
## geneID Count
## GO:0004674 MAPK9/MAPK3/CHEK1/CDK1/EEF2K 5
## GO:0004707 MAPK9/MAPK3 2
## GO:0106310 MAPK9/MAPK3/CHEK1/CDK1 4
## GO:0035173 CHEK1/CDK1 2
## GO:0030544 CDK1/TFRC 2
## GO:0001618 CDK1/TFRC 2
## ID Description GeneRatio
## GO:0042770 GO:0042770 signal transduction in response to DNA damage 5/13
## GO:0051054 GO:0051054 positive regulation of DNA metabolic process 5/13
## GO:0010038 GO:0010038 response to metal ion 5/13
## GO:0046686 GO:0046686 response to cadmium ion 3/13
## GO:0071241 GO:0071241 cellular response to inorganic substance 4/13
## GO:0048308 GO:0048308 organelle inheritance 2/13
## BgRatio pvalue p.adjust qvalue
## GO:0042770 188/18888 1.117445e-07 0.0001108506 5.069672e-05
## GO:0051054 301/18888 1.152338e-06 0.0005715598 2.613989e-04
## GO:0010038 360/18888 2.776478e-06 0.0009180888 4.198814e-04
## GO:0046686 60/18888 8.520614e-06 0.0021131124 9.664171e-04
## GO:0071241 229/18888 1.381094e-05 0.0027400908 1.253161e-03
## GO:0048308 15/18888 4.568487e-05 0.0064741987 2.960929e-03
## geneID Count
## GO:0042770 RAD51/MAPK3/CHEK1/CDK1/FOXM1 5
## GO:0051054 RAD51/MAPK3/CDK1/FOXM1/TFRC 5
## GO:0010038 MAPK9/MAPK3/CDK1/EEF2K/TFRC 5
## GO:0046686 MAPK9/MAPK3/CDK1 3
## GO:0071241 RAD51/MAPK9/MAPK3/EEF2K 4
## GO:0048308 MAPK3/CDK1 2
## ID Description GeneRatio
## GO:0000781 GO:0000781 chromosome, telomeric region 3/13
## GO:0000794 GO:0000794 condensed nuclear chromosome 2/13
## GO:0097122 GO:0097122 cyclin A2-CDK1 complex 1/13
## GO:0097125 GO:0097125 cyclin B1-CDK1 complex 1/13
## GO:0099182 GO:0099182 presynaptic intermediate filament cytoskeleton 1/13
## GO:0098687 GO:0098687 chromosomal region 3/13
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0000781 173/19894 0.0001733635 0.01508262 0.009671858 RAD51/CHEK1/CDK1 3
## GO:0000794 81/19894 0.0012405114 0.02273367 0.014578152 RAD51/CHEK1 2
## GO:0097122 2/19894 0.0013065325 0.02273367 0.014578152 CDK1 1
## GO:0097125 2/19894 0.0013065325 0.02273367 0.014578152 CDK1 1
## GO:0099182 2/19894 0.0013065325 0.02273367 0.014578152 RAD51 1
## GO:0098687 402/19894 0.0020144506 0.02920953 0.018730857 RAD51/CHEK1/CDK1 3
## ID
## GO:0004998 GO:0004998
## GO:0120283 GO:0120283
## GO:0004707 GO:0004707
## GO:0043027 GO:0043027
## GO:0004869 GO:0004869
## GO:0043028 GO:0043028
## Description
## GO:0004998 transferrin receptor activity
## GO:0120283 protein serine/threonine kinase binding
## GO:0004707 MAP kinase activity
## GO:0043027 cysteine-type endopeptidase inhibitor activity involved in apoptotic process
## GO:0004869 cysteine-type endopeptidase inhibitor activity
## GO:0043028 cysteine-type endopeptidase regulator activity involved in apoptotic process
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0004998 1/4 2/18522 0.0004318838 0.01295651 0.004091531 TFRC 1
## GO:0120283 1/4 7/18522 0.0015109813 0.02266472 0.007157280 XIAP 1
## GO:0004707 1/4 16/18522 0.0034511548 0.03234409 0.010213925 MAPK3 1
## GO:0043027 1/4 20/18522 0.0043125460 0.03234409 0.010213925 XIAP 1
## GO:0004869 1/4 37/18522 0.0079672300 0.03961505 0.012510017 XIAP 1
## GO:0043028 1/4 42/18522 0.0090402197 0.03961505 0.012510017 XIAP 1
## ID
## GO:0051054 GO:0051054
## GO:0032872 GO:0032872
## GO:0070302 GO:0070302
## GO:0051403 GO:0051403
## GO:0031098 GO:0031098
## GO:1902528 GO:1902528
## Description
## GO:0051054 positive regulation of DNA metabolic process
## GO:0032872 regulation of stress-activated MAPK cascade
## GO:0070302 regulation of stress-activated protein kinase signaling cascade
## GO:0051403 stress-activated MAPK cascade
## GO:0031098 stress-activated protein kinase signaling cascade
## GO:1902528 regulation of protein linear polyubiquitination
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0051054 3/4 301/18888 1.584016e-05 0.003341572 0.0009517791
## GO:0032872 2/4 35/18888 1.996811e-05 0.003341572 0.0009517791
## GO:0070302 2/4 38/18888 2.358757e-05 0.003341572 0.0009517791
## GO:0051403 2/4 50/18888 4.106724e-05 0.004363395 0.0012428244
## GO:0031098 2/4 59/18888 5.732355e-05 0.004872502 0.0013878333
## GO:1902528 1/4 2/18888 4.235157e-04 0.020667597 0.0058867459
## geneID Count
## GO:0051054 MAPK3/FOXM1/TFRC 3
## GO:0032872 MAPK3/FOXM1 2
## GO:0070302 MAPK3/FOXM1 2
## GO:0051403 MAPK3/FOXM1 2
## GO:0031098 MAPK3/FOXM1 2
## GO:1902528 XIAP 1
## ID Description GeneRatio BgRatio
## GO:1990712 GO:1990712 HFE-transferrin receptor complex 1/4 8/19894
## GO:0005769 GO:0005769 early endosome 2/4 428/19894
## GO:0031143 GO:0031143 pseudopodium 1/4 18/19894
## pvalue p.adjust qvalue geneID Count
## GO:1990712 0.001607676 0.03855515 0.01902392 TFRC 1
## GO:0005769 0.002692287 0.03855515 0.01902392 MAPK3/TFRC 2
## GO:0031143 0.003614545 0.03855515 0.01902392 MAPK3 1barplot(ego_MF[[1]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Deviance")
barplot(ego_MF[[2]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, C-Index")
barplot(ego_MF[[3]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, Deviance")
barplot(ego_MF[[4]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, C-Index")
#barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, C-Index")
barplot(ego_MF[[6]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, Deviance")
barplot(ego_MF[[7]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, C-Index")
barplot(ego_MF[[8]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")
barplot(ego_MF[[9]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, C-Index")
barplot(ego_MF[[10]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, Deviance")
#barplot(ego_MF[[11]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, C-Index")
barplot(ego_BP[[1]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Deviance")
barplot(ego_BP[[2]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, C-Index")
barplot(ego_BP[[3]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, Deviance")
barplot(ego_BP[[4]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, C-Index")
#barplot(ego_BP[[5]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ego_BP[[5]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, C-Index")
barplot(ego_BP[[6]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, Deviance")
barplot(ego_BP[[7]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, C-Index")
barplot(ego_BP[[8]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")
barplot(ego_BP[[9]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, C-Index")
barplot(ego_BP[[10]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, Deviance")
#barplot(ego_BP[[11]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, C-Index")
barplot(ego_CC[[1]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Deviance")
barplot(ego_CC[[2]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, C-Index")
barplot(ego_CC[[3]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, Deviance")
barplot(ego_CC[[4]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, C-Index")
#barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, C-Index")
barplot(ego_CC[[6]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, Deviance")
barplot(ego_CC[[7]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, C-Index")
barplot(ego_CC[[8]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")
barplot(ego_CC[[9]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, C-Index")
barplot(ego_CC[[10]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, Deviance")
#barplot(ego_CC[[11]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, C-Index")DAG plots for ego
goplot(ego_MF[[1]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Deviance")
goplot(ego_MF[[2]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, C-Index")
goplot(ego_MF[[3]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, Deviance")
goplot(ego_MF[[4]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, C-Index")
#goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Deviance")
goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, C-Index")
goplot(ego_MF[[6]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, Deviance")
goplot(ego_MF[[7]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, C-Index")
goplot(ego_MF[[8]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")
goplot(ego_MF[[9]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, C-Index")
goplot(ego_MF[[10]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, Deviance")
#goplot(ego_MF[[11]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, C-Index")
goplot(ego_BP[[1]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Deviance")## Warning: ggrepel: 2 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[2]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, C-Index")## Warning: ggrepel: 9 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[3]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, Deviance")## Warning: ggrepel: 14 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[4]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, C-Index")## Warning: ggrepel: 14 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
#goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Deviance")
goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, C-Index")## Warning: ggrepel: 40 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[6]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, Deviance")## Warning: ggrepel: 14 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[7]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, C-Index")## Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[8]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")## Warning: ggrepel: 9 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[9]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, C-Index")## Warning: ggrepel: 9 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[10]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, Deviance")## Warning: ggrepel: 14 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
#goplot(ego_BP[[11]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, C-Index")
goplot(ego_CC[[1]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Deviance")
goplot(ego_CC[[2]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, C-Index")
goplot(ego_CC[[3]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, Deviance")
goplot(ego_CC[[4]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, C-Index")
#goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Deviance")
goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, C-Index")
goplot(ego_CC[[6]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, Deviance")
goplot(ego_CC[[7]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, C-Index")
goplot(ego_CC[[8]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")
goplot(ego_CC[[9]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, C-Index")
goplot(ego_CC[[10]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, Deviance")
#goplot(ego_CC[[11]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, C-Index")3. Export Pathway Analysis result to data
pathway = list("ggo_MF" = ggo_MF,
"ggo_BP" = ggo_BP,
"ggo_CC" = ggo_CC,
"ego_MF" = ego_MF,
"ego_BP" = ego_BP,
"ego_CC" = ego_CC)
saveRDS(pathway, file = "data/out_pathway/pathways_glmnet_cox_1se.rds")